Fix warnings in tests (#2617)(patch)

Cleaned up some warnings in the tests due to not following the pattern where the caller is supposed to add objects to the session

tests/cli/upload/test_cli_upload_observations.py

@@ -21,7 +21,7 @@
 from cg.meta.observations.mip_dna_observations_api import MipDNAObservationsAPI
 from cg.models.cg_config import CGConfig
 from cg.store import Store
-from cg.store.models import Family, Sample
+from cg.store.models import Family, FamilySample, Sample
 from tests.store_helpers import StoreHelpers
 
 
@@ -143,8 +143,12 @@ def test_get_sequencing_method_exception(
     sample_wes: Sample = helpers.add_sample(
         store, application_tag=external_wes_application_tag, application_type=SequencingMethod.WES
     )
-    link_1 = store.relate_sample(family=case, sample=sample_wgs, status=PhenotypeStatus.UNKNOWN)
-    link_2 = store.relate_sample(family=case, sample=sample_wes, status=PhenotypeStatus.UNKNOWN)
+    link_1: FamilySample = store.relate_sample(
+        family=case, sample=sample_wgs, status=PhenotypeStatus.UNKNOWN
+    )
+    link_2: FamilySample = store.relate_sample(
+        family=case, sample=sample_wes, status=PhenotypeStatus.UNKNOWN
+    )
     store.session.add_all([link_1, link_2])
 
     # WHEN getting the sequencing method

tests/store/api/conftest.py

@@ -9,6 +9,7 @@
 from cg.constants.subject import PhenotypeStatus
 from cg.meta.orders.pool_submitter import PoolSubmitter
 from cg.store import Store
+from cg.store.models import FamilySample
 from tests.meta.demultiplex.conftest import populated_flow_cell_store
 from tests.store_helpers import StoreHelpers
 
@@ -478,9 +479,10 @@ def store_with_analyses_for_cases(
             completed_at=timestamp_now,
         )
         sample = helpers.add_sample(analysis_store, delivered_at=timestamp_now)
-        analysis_store.relate_sample(
+        link: FamilySample = analysis_store.relate_sample(
             family=oldest_analysis.family, sample=sample, status=PhenotypeStatus.UNKNOWN
         )
+        analysis_store.session.add(link)
 
     return analysis_store
 
@@ -517,9 +519,10 @@ def store_with_analyses_for_cases_not_uploaded_fluffy(
             pipeline=Pipeline.FLUFFY,
         )
         sample = helpers.add_sample(analysis_store, delivered_at=timestamp_now)
-        analysis_store.relate_sample(
+        link: FamilySample = analysis_store.relate_sample(
             family=oldest_analysis.family, sample=sample, status=PhenotypeStatus.UNKNOWN
         )
+        analysis_store.session.add(link)
     return analysis_store
 
 
@@ -556,9 +559,10 @@ def store_with_analyses_for_cases_not_uploaded_microsalt(
             pipeline=Pipeline.MICROSALT,
         )
         sample = helpers.add_sample(analysis_store, delivered_at=timestamp_now)
-        analysis_store.relate_sample(
+        link: FamilySample = analysis_store.relate_sample(
             family=oldest_analysis.family, sample=sample, status=PhenotypeStatus.UNKNOWN
         )
+        analysis_store.session.add(link)
     return analysis_store
 
 
@@ -596,8 +600,9 @@ def store_with_analyses_for_cases_to_deliver(
             pipeline=Pipeline.MIP_DNA,
         )
         sample = helpers.add_sample(analysis_store, delivered_at=None)
-        analysis_store.relate_sample(
+        link: FamilySample = analysis_store.relate_sample(
             family=oldest_analysis.family, sample=sample, status=PhenotypeStatus.UNKNOWN
         )
+        analysis_store.session.add(link)
 
     return analysis_store

tests/store/api/status/test_analyses_to_clean.py

@@ -3,6 +3,7 @@
 
 from cg.constants import Pipeline
 from cg.store import Store
+from cg.store.models import FamilySample
 
 
 def test_analysis_included(
@@ -18,7 +19,10 @@ def test_analysis_included(
         cleaned_at=None,
     )
     sample = helpers.add_sample(analysis_store, delivered_at=timestamp_yesterday)
-    analysis_store.relate_sample(family=analysis.family, sample=sample, status="unknown")
+    link: FamilySample = analysis_store.relate_sample(
+        family=analysis.family, sample=sample, status="unknown"
+    )
+    analysis_store.session.add(link)
 
     # WHEN calling the analyses_to_clean
     analyses_to_clean = analysis_store.get_analyses_to_clean(before=timestamp_now)
@@ -35,7 +39,9 @@ def test_analysis_excluded(analysis_store: Store, helpers, timestamp_now: dateti
         analysis_store, started_at=timestamp_now, uploaded_at=None, cleaned_at=None
     )
     sample = helpers.add_sample(analysis_store, delivered_at=timestamp_now)
-    link = analysis_store.relate_sample(family=analysis.family, sample=sample, status="unknown")
+    link: FamilySample = analysis_store.relate_sample(
+        family=analysis.family, sample=sample, status="unknown"
+    )
     analysis_store.session.add(link)
 
     # WHEN calling the analyses_to_clean
@@ -60,7 +66,9 @@ def test_pipeline_included(
         cleaned_at=None,
     )
     sample = helpers.add_sample(analysis_store, delivered_at=timestamp_yesterday)
-    link = analysis_store.relate_sample(family=analysis.family, sample=sample, status="unknown")
+    link: FamilySample = analysis_store.relate_sample(
+        family=analysis.family, sample=sample, status="unknown"
+    )
     analysis_store.session.add(link)
 
     # WHEN calling the analyses_to_clean specifying the used pipeline
@@ -87,7 +95,9 @@ def test_pipeline_excluded(analysis_store: Store, helpers, timestamp_now: dateti
         cleaned_at=None,
     )
     sample = helpers.add_sample(analysis_store, delivered_at=timestamp_now)
-    link = analysis_store.relate_sample(family=analysis.family, sample=sample, status="unknown")
+    link: FamilySample = analysis_store.relate_sample(
+        family=analysis.family, sample=sample, status="unknown"
+    )
     analysis_store.session.add(link)
 
     # WHEN calling the analyses_to_clean specifying another pipeline
@@ -110,7 +120,9 @@ def test_non_cleaned_included(
         cleaned_at=None,
     )
     sample = helpers.add_sample(analysis_store, delivered_at=timestamp_yesterday)
-    link = analysis_store.relate_sample(family=analysis.family, sample=sample, status="unknown")
+    link: FamilySample = analysis_store.relate_sample(
+        family=analysis.family, sample=sample, status="unknown"
+    )
     analysis_store.session.add(link)
 
     # WHEN calling the analyses_to_clean
@@ -131,7 +143,9 @@ def test_cleaned_excluded(analysis_store: Store, helpers, timestamp_now: datetim
         cleaned_at=timestamp_now,
     )
     sample = helpers.add_sample(analysis_store, delivered_at=timestamp_now)
-    link = analysis_store.relate_sample(family=analysis.family, sample=sample, status="unknown")
+    link: FamilySample = analysis_store.relate_sample(
+        family=analysis.family, sample=sample, status="unknown"
+    )
     analysis_store.session.add(link)
 
     # WHEN calling the analyses_to_clean

tests/store/api/status/test_analyses_to_delivery_report.py

@@ -3,6 +3,7 @@
 from cg.constants import DataDelivery, Pipeline
 from cg.constants.subject import PhenotypeStatus
 from cg.store import Store
+from cg.store.models import FamilySample
 from cg.utils.date import get_date
 
 
@@ -20,7 +21,7 @@ def test_missing(analysis_store: Store, helpers, timestamp_now):
         data_delivery=DataDelivery.SCOUT,
     )
     sample = helpers.add_sample(analysis_store, delivered_at=timestamp_now)
-    link = analysis_store.relate_sample(
+    link: FamilySample = analysis_store.relate_sample(
         family=analysis.family, sample=sample, status=PhenotypeStatus.UNKNOWN
     )
     analysis_store.session.add(link)
@@ -56,9 +57,10 @@ def test_outdated_analysis(analysis_store, helpers, timestamp_now, timestamp_yes
     sample = helpers.add_sample(analysis_store, delivered_at=timestamp_now)
 
     # GIVEN a store sample case relation
-    analysis_store.relate_sample(
+    link: FamilySample = analysis_store.relate_sample(
         family=analysis.family, sample=sample, status=PhenotypeStatus.UNKNOWN
     )
+    analysis_store.session.add(link)
 
     # WHEN calling the analyses_to_delivery_report
     analyses = analysis_store.analyses_to_delivery_report(pipeline=pipeline).all()

tests/store/api/status/test_store_api_status_analysis.py

@@ -8,7 +8,7 @@
 from cg.constants.constants import CaseActions
 from cg.constants.subject import PhenotypeStatus
 from cg.store import Store
-from cg.store.models import Analysis, Family, Sample
+from cg.store.models import Analysis, Family, FamilySample, Sample
 from tests.store_helpers import StoreHelpers
 
 
@@ -301,8 +301,13 @@ def test_one_of_two_sequenced_samples(
     not_sequenced_sample: Sample = helpers.add_sample(base_store, reads_updated_at=None)
 
     # GIVEN a database with a case with one of one sequenced samples and no analysis
-    base_store.relate_sample(test_case, sequenced_sample, PhenotypeStatus.UNKNOWN)
-    base_store.relate_sample(test_case, not_sequenced_sample, PhenotypeStatus.UNKNOWN)
+    link_1: FamilySample = base_store.relate_sample(
+        test_case, sequenced_sample, PhenotypeStatus.UNKNOWN
+    )
+    link_2: FamilySample = base_store.relate_sample(
+        test_case, not_sequenced_sample, PhenotypeStatus.UNKNOWN
+    )
+    base_store.session.add_all([link_1, link_2])
 
     # WHEN getting cases to analyse
     cases: list[Family] = base_store.cases_to_analyze(pipeline=Pipeline.MIP_DNA, threshold=True)

tests/store/api/status/test_store_api_status_cases.py

@@ -2,7 +2,7 @@
 
 from cg.constants import CASE_ACTIONS, DataDelivery, Pipeline, Priority
 from cg.store import Store
-from cg.store.models import Analysis, Family
+from cg.store.models import Analysis, Family, FamilySample
 
 
 def test_delivered_at_affects_tat(base_store: Store, helpers):
@@ -113,10 +113,10 @@ def test_samples_flowcell(base_store: Store, helpers):
     new_case = add_case(helpers, base_store)
     sample_on_flowcell = helpers.add_sample(base_store)
     flowcell = helpers.add_flow_cell(base_store, samples=[sample_on_flowcell], status="ondisk")
-    link_1 = base_store.relate_sample(new_case, sample_on_flowcell, "unknown")
+    link_1: FamilySample = base_store.relate_sample(new_case, sample_on_flowcell, "unknown")
     base_store.session.add(link_1)
     sample_not_on_flowcell = helpers.add_sample(base_store)
-    link_2 = base_store.relate_sample(new_case, sample_not_on_flowcell, "unknown")
+    link_2: FamilySample = base_store.relate_sample(new_case, sample_not_on_flowcell, "unknown")
     base_store.session.add(link_2)
 
     # WHEN getting active cases
@@ -198,8 +198,8 @@ def test_received_at_is_newest_date(base_store: Store, helpers):
     yesteryear = datetime.now() - timedelta(days=365)
     newest_sample = helpers.add_sample(base_store, received_at=yesterday)
     oldest_sample = helpers.add_sample(base_store, received_at=yesteryear)
-    link_1 = base_store.relate_sample(new_case, newest_sample, "unknown")
-    link_2 = base_store.relate_sample(new_case, oldest_sample, "unknown")
+    link_1: FamilySample = base_store.relate_sample(new_case, newest_sample, "unknown")
+    link_2: FamilySample = base_store.relate_sample(new_case, oldest_sample, "unknown")
     base_store.session.add_all([link_1, link_2])
 
     # WHEN getting active cases
@@ -220,8 +220,8 @@ def test_prepared_at_is_newest_date(base_store: Store, helpers):
     yesteryear = datetime.now() - timedelta(days=365)
     newest_sample = helpers.add_sample(base_store, prepared_at=yesterday)
     oldest_sample = helpers.add_sample(base_store, prepared_at=yesteryear)
-    link_1 = base_store.relate_sample(new_case, newest_sample, "unknown")
-    link_2 = base_store.relate_sample(new_case, oldest_sample, "unknown")
+    link_1: FamilySample = base_store.relate_sample(new_case, newest_sample, "unknown")
+    link_2: FamilySample = base_store.relate_sample(new_case, oldest_sample, "unknown")
     base_store.session.add_all([link_1, link_2])
 
     # WHEN getting active cases
@@ -242,8 +242,8 @@ def test_sequenced_at_is_newest_date(base_store: Store, helpers):
     yesteryear = datetime.now() - timedelta(days=365)
     newest_sample = helpers.add_sample(base_store, reads_updated_at=yesterday)
     oldest_sample = helpers.add_sample(base_store, reads_updated_at=yesteryear)
-    link_1 = base_store.relate_sample(new_case, newest_sample, "unknown")
-    link_2 = base_store.relate_sample(new_case, oldest_sample, "unknown")
+    link_1: FamilySample = base_store.relate_sample(new_case, newest_sample, "unknown")
+    link_2: FamilySample = base_store.relate_sample(new_case, oldest_sample, "unknown")
     base_store.session.add_all([link_1, link_2])
 
     # WHEN getting active cases
@@ -264,8 +264,8 @@ def test_delivered_at_is_newest_date(base_store: Store, helpers):
     yesteryear = datetime.now() - timedelta(days=365)
     newest_sample = helpers.add_sample(base_store, delivered_at=yesterday)
     oldest_sample = helpers.add_sample(base_store, delivered_at=yesteryear)
-    link_1 = base_store.relate_sample(new_case, newest_sample, "unknown")
-    link_2 = base_store.relate_sample(new_case, oldest_sample, "unknown")
+    link_1: FamilySample = base_store.relate_sample(new_case, newest_sample, "unknown")
+    link_2: FamilySample = base_store.relate_sample(new_case, oldest_sample, "unknown")
     base_store.session.add_all([link_1, link_2])
 
     # WHEN getting active cases
@@ -292,8 +292,8 @@ def test_invoiced_at_is_newest_invoice_date(base_store: Store, helpers):
     invoice = base_store.add_invoice(helpers.ensure_customer(base_store))
     oldest_sample.invoice = invoice
     oldest_sample.invoice.invoiced_at = yesteryear
-    link_1 = base_store.relate_sample(new_case, newest_sample, "unknown")
-    link_2 = base_store.relate_sample(new_case, oldest_sample, "unknown")
+    link_1: FamilySample = base_store.relate_sample(new_case, newest_sample, "unknown")
+    link_2: FamilySample = base_store.relate_sample(new_case, oldest_sample, "unknown")
     base_store.session.add_all([link_1, link_2])
 
     # WHEN getting active cases
@@ -598,11 +598,14 @@ def test_show_multiple_data_analysis(base_store: Store, helpers):
     data_analysis = Pipeline.BALSAMIC
     new_case = add_case(helpers, base_store, data_analysis=data_analysis)
     sample1 = helpers.add_sample(base_store)
-    base_store.relate_sample(new_case, sample1, "unknown")
+    link_1: FamilySample = base_store.relate_sample(new_case, sample1, "unknown")
+    base_store.session.add(link_1)
     new_case2 = add_case(helpers, base_store, case_id="new_case2", data_analysis=data_analysis)
     sample2 = helpers.add_sample(base_store)
-    base_store.relate_sample(new_case, sample2, "unknown")
-    base_store.relate_sample(new_case2, sample2, "unknown")
+    link_2: FamilySample = base_store.relate_sample(new_case, sample2, "unknown")
+    link_3: FamilySample = base_store.relate_sample(new_case2, sample2, "unknown")
+    base_store.session.add_all([link_2, link_3])
+    base_store.session.commit()
 
     # WHEN getting active cases by data_analysis
     cases = base_store.cases(data_analysis=str(data_analysis)[:-1])
@@ -826,7 +829,8 @@ def test_only_prepared_cases(base_store: Store, helpers):
     base_store.session.add(link)
     neg_new_case = add_case(helpers, base_store, "neg_new_case")
     neg_sample = helpers.add_sample(base_store, name="neg_sample")
-    base_store.relate_sample(neg_new_case, neg_sample, "unknown")
+    link = base_store.relate_sample(neg_new_case, neg_sample, "unknown")
+    base_store.session.add(link)
 
     # WHEN getting active cases excluding prepared
     cases = base_store.cases(only_prepared=True)
@@ -847,7 +851,8 @@ def test_only_received_cases(base_store: Store, helpers):
     base_store.session.add(link)
     neg_new_case = add_case(helpers, base_store, "neg_new_case")
     neg_sample = helpers.add_sample(base_store, name="neg_sample")
-    base_store.relate_sample(neg_new_case, neg_sample, "unknown")
+    link = base_store.relate_sample(neg_new_case, neg_sample, "unknown")
+    base_store.session.add(link)
 
     # WHEN getting active cases excluding received
     cases = base_store.cases(only_received=True)
@@ -868,7 +873,8 @@ def test_only_sequenced_cases(base_store: Store, helpers):
     base_store.session.add(link)
     neg_new_case = add_case(helpers, base_store, "neg_new_case")
     neg_sample = helpers.add_sample(base_store, name="neg_sample")
-    base_store.relate_sample(neg_new_case, neg_sample, "unknown")
+    link = base_store.relate_sample(neg_new_case, neg_sample, "unknown")
+    base_store.session.add(link)
 
     # WHEN getting active cases excluding sequenced
     cases = base_store.cases(only_sequenced=True)
@@ -889,7 +895,8 @@ def test_only_delivered_cases(base_store: Store, helpers):
     base_store.session.add(link)
     neg_new_case = add_case(helpers, base_store, "neg_new_case")
     neg_sample = helpers.add_sample(base_store, name="neg_sample")
-    base_store.relate_sample(neg_new_case, neg_sample, "unknown")
+    link = base_store.relate_sample(neg_new_case, neg_sample, "unknown")
+    base_store.session.add(link)
 
     # WHEN getting active cases excluding delivered
     cases = base_store.cases(only_delivered=True)
@@ -907,7 +914,8 @@ def test_only_uploaded_cases(base_store: Store, helpers):
     helpers.add_analysis(base_store, uploaded_at=datetime.now())
     neg_new_case = add_case(helpers, base_store, "neg_new_case")
     neg_sample = helpers.add_sample(base_store, name="neg_sample")
-    base_store.relate_sample(neg_new_case, neg_sample, "unknown")
+    link = base_store.relate_sample(neg_new_case, neg_sample, "unknown")
+    base_store.session.add(link)
 
     # WHEN getting active cases excluding uploaded
     cases = base_store.cases(only_uploaded=True)
@@ -925,7 +933,8 @@ def test_only_delivery_reported_cases(base_store: Store, helpers):
     helpers.add_analysis(base_store, delivery_reported_at=datetime.now())
     neg_new_case = add_case(helpers, base_store, "neg_new_case")
     neg_sample = helpers.add_sample(base_store, name="neg_sample")
-    base_store.relate_sample(neg_new_case, neg_sample, "unknown")
+    link = base_store.relate_sample(neg_new_case, neg_sample, "unknown")
+    base_store.session.add(link)
 
     # WHEN getting active cases excluding delivery_reported
     cases = base_store.cases(only_delivery_reported=True)
@@ -948,7 +957,8 @@ def test_only_invoiced_cases(base_store: Store, helpers):
     base_store.session.add(link)
     neg_new_case = add_case(helpers, base_store, "neg_new_case")
     neg_sample = helpers.add_sample(base_store, name="neg_sample")
-    base_store.relate_sample(neg_new_case, neg_sample, "unknown")
+    link = base_store.relate_sample(neg_new_case, neg_sample, "unknown")
+    base_store.session.add(link)
 
     # WHEN getting active cases excluding invoiced
     cases = base_store.cases(only_invoiced=True)
@@ -966,7 +976,8 @@ def test_only_analysed_cases(base_store: Store, helpers):
     helpers.add_analysis(base_store, completed_at=datetime.now())
     neg_new_case = add_case(helpers, base_store, "neg_new_case")
     neg_sample = helpers.add_sample(base_store, name="neg_sample")
-    base_store.relate_sample(neg_new_case, neg_sample, "unknown")
+    link = base_store.relate_sample(neg_new_case, neg_sample, "unknown")
+    base_store.session.add(link)
 
     # WHEN getting active cases excluding not analysed
     cases = base_store.cases(only_analysed=True)
@@ -1331,8 +1342,8 @@ def test_one_of_two_samples_received(base_store: Store, helpers):
     new_case = add_case(helpers, base_store)
     sample_received = helpers.add_sample(base_store, "sample_received", received_at=datetime.now())
     sample_not_received = helpers.add_sample(base_store, "sample_not_received", received_at=None)
-    link_1 = base_store.relate_sample(new_case, sample_received, "unknown")
-    link_2 = base_store.relate_sample(new_case, sample_not_received, "unknown")
+    link_1: FamilySample = base_store.relate_sample(new_case, sample_received, "unknown")
+    link_2: FamilySample = base_store.relate_sample(new_case, sample_not_received, "unknown")
     base_store.session.add_all([link_1, link_2])
     assert sample_received.received_at is not None
     assert sample_not_received.received_at is None